Difference between revisions of "SMRT Analyis: The input.xml file"
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= The input.xml file = | = The input.xml file = | ||
| − | In order to run the smrtpipe program, an input.xml file must be included. This XML file contains the filenames of the bas.h5/bax.h5 read files to be used by the pipeline. The fofnToSmrtpipeInput.py script, included in the smrtanalysis package, can create this XML file. It needs a file-of-filenames (fofn) file as input. The fofn file is simply a text file containing one filename per line, for instance: | + | In order to run the smrtpipe program, an input.xml file must be included. This XML file contains the filenames of the bas.h5/bax.h5 read files to be used by the pipeline. The <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py</span> script, included in the smrtanalysis package, can create this XML file. It needs a file-of-filenames (fofn) file as input. The fofn file is simply a text file containing one filename per line, for instance: |
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| − | This text file is transformed to a XML file using the fofnToSmrtpipeInput.py script: | + | This text file is transformed to a XML file using the <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py</span> script: |
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| − | <span style="font-family:courier new,courier,monospace;"><?xml version="1.0"?> | + | <span style="font-family:courier new,courier,monospace;"><?xml version="1.0"?></span> |
<span style="font-family:courier new,courier,monospace;"><pacbioAnalysisInputs></span> | <span style="font-family:courier new,courier,monospace;"><pacbioAnalysisInputs></span> | ||
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<span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0000"><location>/path/to/first_bax.h5</location></url></span> | <span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0000"><location>/path/to/first_bax.h5</location></url></span> | ||
| − | <span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0001"><location>/path/to/second_bax.h5</location></url> | + | <span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0001"><location>/path/to/second_bax.h5</location></url></span> |
<span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0002"><location>/path/to/third_bax.h5</location></url></span> | <span style="font-family:courier new,courier,monospace;"> <url ref="run:0000000-0002"><location>/path/to/third_bax.h5</location></url></span> | ||
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<span style="font-family:courier new,courier,monospace;"> </span> | <span style="font-family:courier new,courier,monospace;"> </span> | ||
| − | The fofnToSmrtpipeInput.py script can also specify an id, name, and comment for the smrtpipe job to be run. See fofnToSmrtpipeInput.py –h for details. | + | The <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py</span> script can also specify an id, name, and comment for the smrtpipe job to be run. See <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py –h</span> for details. |
| − | In addition to containing bas.h5/bax.h5 files, the input.xml can also specify filenames of fastq or fasta files (as the fofnToSmrtpipeInput.py script does not support this, such an input.xml must be manually created): | + | In addition to containing bas.h5/bax.h5 files, the input.xml can also specify filenames of fastq or fasta files (as the <span style="font-family:courier new,courier,monospace;">fofnToSmrtpipeInput.py</span> script does not support this, such an input.xml must be manually created): |
Revision as of 15:18, 9 March 2015
The input.xml file
In order to run the smrtpipe program, an input.xml file must be included. This XML file contains the filenames of the bas.h5/bax.h5 read files to be used by the pipeline. The fofnToSmrtpipeInput.py script, included in the smrtanalysis package, can create this XML file. It needs a file-of-filenames (fofn) file as input. The fofn file is simply a text file containing one filename per line, for instance:
/path/to/first_bax.h5
/path/to/second_bax.h5
/path/to/third_bax.h5
This text file is transformed to a XML file using the fofnToSmrtpipeInput.py script:
module load smrtanalysis/2.3.0
fofnToSmrtpipeInput.py /path/to/fofn.txt > input.xml
The resulting input.xml file:
<?xml version="1.0"?>
<pacbioAnalysisInputs>
<dataReferences>
<url ref="run:0000000-0000"><location>/path/to/first_bax.h5</location></url>
<url ref="run:0000000-0001"><location>/path/to/second_bax.h5</location></url>
<url ref="run:0000000-0002"><location>/path/to/third_bax.h5</location></url>
</dataReferences>
</pacbioAnalysisInputs>
The fofnToSmrtpipeInput.py script can also specify an id, name, and comment for the smrtpipe job to be run. See fofnToSmrtpipeInput.py –h for details.
In addition to containing bas.h5/bax.h5 files, the input.xml can also specify filenames of fastq or fasta files (as the fofnToSmrtpipeInput.py script does not support this, such an input.xml must be manually created):
<?xml version="1.0"?>
<pacbioAnalysisInputs>
<dataReferences>
<url ref="run:0000000-0001"><location>/path/to/bax.h5</location></url>
<url ref="fastq:/path/to/Fastq"/>
</dataReferences>
</pacbioAnalysisInputs>
